lme4 v1.1-5

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by Ben Bolker

Linear mixed-effects models using Eigen and S4

Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the Eigen C++ library for numerical linear algebra and RcppEigen "glue".

Functions in lme4

Name Description
GHrule Univariate Gauss-Hermite quadrature rule
bootMer Model-based (Semi-)Parametric Bootstrap for Mixed Models
isNested Is f1 nested within f2?
glmer Fit Generalized Linear Mixed-Effects Models
VarCorr Extract Variance and Correlation Components
golden Generator object for the golden search optimizer class.
cake Breakage Angle of Chocolate Cakes
glmFamily Generator object for the glmFamily class
glmer.nb glmer() for Negative Binomial
findbars Determine random-effects expressions from a formula
fixef Extract fixed-effects estimates
mkReTrms Create Z, Lambda, Lind, etc.
Pastes Paste strength by batch and cask
isREML Check characteristics of models
lmResp-class Classes "lmResp", "glmResp", "nlsResp" and "lmerResp"
lme4-package Linear, generalized linear, and nonlinear mixed models
InstEval University Lecture/Instructor Evaluations by Students at ETH
dummy Dummy variables (experimental)
GQdk Sparse Gaussian Quadrature grid
getME Extract or Get Generalized Components from a Fitted Mixed Effects Model
varianceProf Transform to the variance scale
pvalues Getting p-values for fitted models
mkVarCorr Make Variance and Correlation Matrices from theta
ranef Extract the modes of the random effects
refit Refit a model with a new response, by maximum likelihood criterion
Penicillin Variation in penicillin testing
fortify add information to data based on a fitted model
ngrps Number of levels
plot.merMod diagnostic plots for merMod fits
merPredD Generator object for the merPredD class
lmerControl Control of Mixed Model Fitting
simulate.merMod Simulate responses from a merMod object
rePos Generator object for the rePos (random-effects positions) class
devcomp Extract the deviance component list
expandDoubleVerts Expand terms with '||' notation into separate '|' terms
nobars Omit terms separated by vertical bars in a formula
merPredD-class Class "merPredD" - a dense predictor reference class
confint.merMod Compute confidence intervals on the parameters of an lme4 fit
merMod-class Class "merMod" of Fitted Mixed-Effect Models
drop1.merMod Drop all possible single fixed-effect terms from a mixed effect model
nlmer Fit Nonlinear Mixed-Effects Models
nlformula Manipulate a nonlinear model formula.
profile-methods Profile method for merMod objects
residuals.merMod residuals of merMod objects
NelderMead Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained
sleepstudy Reaction times in a sleep deprivation study
Dyestuff Yield of dyestuff by batch
modular Modular functions for mixed model fits
predict.merMod Predictions from a model at new data values
lmList List of lm Objects with a Common Model
lmList-class Class "lmList" of 'lm' Objects on Common Model
mkMerMod Create a merMod object
lmer Fit Linear Mixed-Effects Models
refitML Refit a model by maximum likelihood criterion
rePos-class Class "rePos"
GQN Sparse Gauss-Hermite quadrature grids
VerbAgg Verbal Aggression item responses
golden-class Class "golden"
plots.thpr Mixed-Effects Profile Plots (Regular / Density / Pairs)
mkRespMod Create an lmerResp, glmResp or nlsResp instance
sigma Extract residual standard error
NelderMead-class Class "NelderMead" of Nelder-Mead optimizers and its Generator
grouseticks Data on red grouse ticks from Elston et al. 2001
subbars "Sub[stitute] Bars"
cbpp Contagious bovine pleuropneumonia
glmFamily-class Class "glmFamily" - a reference class for family
lmResp Generator objects for the response classes
mkdevfun Create a deviance evaluation function from a predictor and a response module
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